Plot a pseudobulk genome track, showing the number of fragment insertions across a region.
Usage
trackplot_bulk(
fragments,
region,
groups,
cell_read_counts,
group_order = NULL,
bins = 200,
clip_quantile = 0.999,
colors = discrete_palette("stallion"),
legend_label = "group",
zero_based_coords = !is(region, "GRanges"),
return_data = FALSE,
return_plot_list = FALSE,
apply_styling = TRUE
)Arguments
- fragments
Fragments object
- region
GRanges of length 1 with region to plot, or list/data.frame with one entry each for chr, start, end. See
gene_region()or genomic-ranges for details- groups
Vector with one entry per cell, specifying the cell's group
- cell_read_counts
Numeric vector of read counts for each cell (used for normalization)
- group_order
Optional vector listing ordering of groups
- bins
Number of bins to plot across the region
- clip_quantile
(optional) Quantile of values for clipping y-axis limits. Default of 0.999 will crop out just the most extreme outliers across the region. NULL to disable clipping
- colors
Character vector of color values (optionally named by group)
- legend_label
Custom label to put on the legend
- zero_based_coords
Whether to convert the ranges from a 1-based end-inclusive coordinate system to a 0-based end-exclusive coordinate system. Defaults to true for GRanges and false for other formats (see this archived UCSC blogpost)
- return_data
If true, return data from just before plotting rather than a plot.
- return_plot_list
If
TRUE, return multiple plots as a list, rather than a single plot combined using patchwork::wrap_plots()- apply_styling
If false, return a plot without pretty styling applied
Value
Returns a combined plot of pseudobulk genome tracks. For compatability with
draw_trackplot_grid(), the extra attribute $patches$labels will be added to
specify the labels for each track. If return_data or return_plot_list is
TRUE, the return value will be modified accordingly.
